A dairy farmer’s application to install a water-efficient irrigation system has been caught up in a controversy over the Victorian Government’s new native vegetation clearing rules.

The Goulburn Valley Environment Group objected last week to Stuart Rea’s application to remove nine grey box trees on his Toolamba property in order to install two centre pivots.

Grey box woodlands vegetation communities are listed as endangered and protected under federal legislation and GVEG president John Pettigrew said the objection was made as a matter of principle.

‘‘It’s not that black and white. We don’t want to start a blue with the farmer,’’ Mr Pettigrew said.

‘‘It’s more about the government’s regulations.’’

Mr Pettigrew labelled the government as irresponsible and said the new rules were based on ‘‘deeply flawed’’ mapping.

One of the flaws found by ecologists was the Calder Park raceway being found in a ‘‘high’’ risk area when the mapping was first introduced in December.

Under the new rules, vegetation mapped in low risk areas and less than a hectare in size no longer requires on-site assessment, and environmentalists fear this will see endangered flora removed.

‘‘The government, by its own admission, knows this, but they are failing to protect scant native vegetation in our region leading to the loss of large trees and habitat for threatened species,’’ Mr Pettigrew said.

Mr Rea submitted his whole farm plan to Greater Shepparton City Council in March, and included an application for the clearing.

Until now, he said he was not fully aware of the debate the new mapping had created between environment groups and political parties.

Mr Pettigrew said GVEG was not against Mr Rea’s irrigation plan.

‘‘We are not anti-development — it depends on how the loss of those trees are compensated,’’ Mr Pettigrew said.

Under the new rules, Mr Rea would not be given any clear offsetting requirements until the application was approved by the council and DEPI.

‘‘There had been discussions of a significant number of trees and land that would be offset and we would abide by any requirements and conditions for this project to go ahead,’’ Mr Rea said.

‘‘I’m also planning to plant another tree line, which won’t be part of the offsetting, to create windbreaks for the pivots.

‘‘I believe the long-term environment benefits of my project, with water savings and tree planting, will outweigh any environment loss of removing the trees.’’

A Greater Shepparton City Council planning spokesperson said Mr Rea’s application was one of the council’s first of such a scale under the government’s new provisions.

The spokesperson said there had been no other objections to the application and council was considering GVEG’s objection and speaking with Mr Rea.